Possible to use denoised tomograms for template matching?

Matthias Vorländer

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Jun 30, 2021, 7:32:52 AM6/30/21

to Warp

Hi there,

I am wondering if it is possible to use the denoised tomograms for template matching in warp? I just think the difference is so spectacular that it seems a shame not to make use of it (see attached images).

Thanks a lot,

Matthias

Pranav Shah

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Jun 30, 2021, 8:17:35 AM6/30/21

to Matthias Vorländer, Warp

Woow! That looks really good! Give it a go and tell us if it worked! Also, how did you make Noise2Map work for you? I have had practically 0 success on a couple of datasets that I have!

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

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Matthias Vorländer

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Jun 30, 2021, 8:38:34 AM6/30/21

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Hi Pranav,

Thanks! Well, I just followed the instructions on the warp website. I am using 10000 iterations. Maybe its related to how much signal you still get in the reconstructions from only odd/even tilts? I am lucky to have huge particles in very thin ice, which might help.

To make it work, would you just replace the tomos in the reconstruciton folder with the denoised ones?

Thanks,

Matthias

Pranav Shah

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Jul 1, 2021, 4:28:33 PM7/1/21

to Warp

Yeah, I suppose thats how i would do it i.e. putting the denoised versions in the reconstruction folder (before backing it up ofc)

Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/7e650923-fe15-4256-b329-a1d9b550630cn%40googlegroups.com.

Matthias Vorländer

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Sep 8, 2021, 8:14:42 AM9/8/21

to Warp

Just for completeness, I did exactly that (replace the tomos in the reconstructtion folder with the denoised versions) and it worked quiet well!